And in the end, maybe what it comes down to is: Categories should not serve as "warning" flags. They are meant to just be taxonomic devices.
Agreed. If someone reads an article on, say, homeopathy and only realizes when she sees the categories at the bottom that the thing doesn't work then there's something wrong with the article (incidentally I think [[homeopathy]] makes the "doesn't work" part fairly clear as it is).
I think rejecting this particular useful category on grounds of the NPOV-policy is a bit too much. Almost every category could be questioned by someone. For a random example I see that the article on the Church of Jesus Christ of the Latter-day Saints is in the "Christian denominations" category. There are Christians that think Mormons aren't Christians.
As for the "alternative medicine" category then I suppose "medicine that has not been proven to work" or some such would be more accurate. I for one would actually prefer "quack medicine" since "alternative" has some undeserved positive connotations and implies that quackery is somehow a viable alternative to actual medicine.
So, don't forget to take the Grumpy Scientist Point of View into account :)
Regards, Haukur Þorgeirsson (User:Haukurth)